Proteins reconstruction

Figure Bl.17.11. Reconstructed density of an a,p-tiibulin protein dimer as obtained from electron crystallography (Nogales etal 1997). Note the appearance of the p-sheets ((a), marked B) and the a-helices ((b), marked H) in the density. In particular the right-handed a-helix H6 is very clear. Pictures by courtesy of E Nogales and Academic Press.

By applying a pulling force at a portion of the solute molecule in a specific direction (see chapters of Eichinger et al. and Schulten in this volume), conformational transitions can be induced in specific directions. In order to reconstruct information about the underlying potential function governing protein motion, the irreversible work performed on the system by these forces must be discounted ([Balsera et al. 1997]). 

Amadei et al. 1993] Amadei, A., Linssen, A.B.M., Berendsen, H.J.C. Essential Dynamics of Proteins. Proteins 17 (1993) 412-425 [Balsera et al. 1997] Balsera, M., Stepaniants, S., Izrailev, S., Oono, Y., Schiilten, K. Reconstructing Potential Energy Functions from Simulated Force-Induced Unbinding Processes. Biophys. J. 73 (1997) 1281-1287 [Case 1996] Case, D.A. Normal mode analysis of protein dynamics. Curr. Op. Struct. Biol. 4 (1994) 285-290... 

This electron microscopy reconstruction has since been extended to high resolution (3 A) where the connections between the helices and the bound retinal molecule are visible together with the seven helices (Figure 12.3c). The helices are tilted by about 20° with respect to the plane of the membrane. This is the first example of a high-resolution three-dimensional protein structure determination using electron microscopy. The structure has subsequently been confirmed by x-ray crystallographic studies to 2 A resolution. 

The overall amino acid sequence of the protein is reconstructed from the sequences in overlapping fragments. 

Introduction of heme residues and different artificial receptors in protein molecules in chemical modification of structures and functions of proteins by the cofactor reconstruction method 99Ef0539. 

We proposed to study diet and health by combining bone chemistry and histomorphometry. Diet would be determined by analysis of stable isotopes of carbon and nitrogen in bone protein and some preserved hair. In addition, trace elements would be quantitatively analyzed in preserved bone mineral. Abonyi (1993) participated in the study by reconstructing the diet from historical sources and analyzing various foods. Having analyzed human tissues for stable isotopes and trace elements, and foods for the same variables, we hoped to learn more about 19th century diet in southern Ontario, and at the same time, learn more about paleodiet reconstruction. 

In the biosynthetic approach, protein expression in E. coli [27], yeast [28, 29], and plants [30, 31] have been employed. This approach requires the construction of genes encoding for these repetitive polypeptides. Different methods for gene construction have been pubhshed multimerization [32], recursive directional ligation [33], and recursive directional ligation via plasmid reconstruction [23, 34]. 

In another study, the original repetitive Cio, (AGAGAGPEG)io, center was reconstructed into nine repeats of AGAGAGPEG with three distributed repeats of the RGD sequence. The new triblock protein, composed of acidic and basic terminal domains in addition to the reconstructed central block, has been shown to support adhesion, spreading, and polarization of human fibroblast cells [82]. Triblock polypeptides that facilitate antibody binding have also been reported [83]. 

FIG. 1 Freeze-etching image of a bacterial cell of (a) Desulfotomaculum nigrificans (bar, 100 nm). Atomic force micrographs of the S-layer proteins of (b) Bacillus sphaericus CCM 2177 and (c) Bacillus stearothermophilus PV72/p2 recrystallized in monolayers on silicon wafers. Bars, 50 nm. The insets in (b) and (c) show the corresponding computer-image reconstructions. 

Doolitde RF Reconstructing history with amino acid sequences. Protein Sci 1992 1 191. 

Fig. 1. Reconstruction of the cell-free protein synthesizing system with the partially purified wheat germ extracts. Control normal wheat germ cell-free system, (I) 0 - 40 % ammonium sulfate fraction 3 pi, 40 - 60 % ammonium sulfate fraction 4 pi, and ribosome 3 pi were added to 25 pi reaction mixture, (II) 0-40 % ammonium sulfate fraction 4 pi, 40 - 60 % ammonium sulfate fraction 4 pi, and ribosome 1.5 pi were added to 25 pi reaction mixture.

DW Urry, A Pattanaik. Elastic protein-based materials in tissue reconstruction. Ann NY Acad Sci 831 32-46, 1997. 

Because protein ROA spectra contain bands characteristic of loops and turns in addition to bands characteristic of secondary structure, they should provide information on the overall three-dimensional solution structure. We are developing a pattern recognition program, based on principal component analysis (PCA), to identify protein folds from ROA spectral band patterns (Blanch etal., 2002b). The method is similar to one developed for the determination of the structure of proteins from VCD (Pancoska etal., 1991) and UVCD (Venyaminov and Yang, 1996) spectra, but is expected to provide enhanced discrimination between different structural types since protein ROA spectra contain many more structure-sensitive bands than do either VCD or UVCD. From the ROA spectral data, the PCA program calculates a set of subspectra that serve as basis functions, the algebraic combination of which with appropriate expansion coefficients can be used to reconstruct any member of the... 

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